Once Upon a Mystery
by McEvoyer
Summary: A Storybrooke resident goes missing and it's up to Emma and her parents to find out what happened. But is there something bigger going on than any of them originally thought? Just something different I wanted to try!
1. Chapter 1

**Hey there! Okay, so this is totally different than what I normally do even though I'm sure I will find a way of interjecting my take on the Charming Family into it somehow! Haha and just to clarify, everyone is still alive – no one fell through a portal or turned into a little boy so we still have Neal and August! I just wanted to try something new – and what could be more different than a mystery? I hope you all enjoy :)**

**Alas, I do not own OUAT.**

Emma was at the table when her phone buzzed. Her spoonful of cereal mid-air, she deliberated over whether to answer it or not, really not in the mood for a conversation right now. Taking a chance, she shovelled the cereal into her mouth and checked the caller I.D.

Regina.

Ugh, she _had _to answer it.

"Hello?" she answered with her mouth full.

"Am I disturbing you Miss Swan?"

Emma rolled her eyes and placed down her spoon. "What is it, Regina?"

Regina hesitated on the other end and unconsciously, Emma sat forward, leaning an elbow on the table, curious. "It's Dr. Hopper," the brunette declared. "He's missing."

"What do you mean he's missing?"

Regina scoffed. "Do I need to look up a dictionary for you? It means that he's not in his office and there's no sign of him around town."

Rising from her chair, Emma wedged the phone between her shoulder and her ear as she carried her bowl and glass over to the sink. "Well have you checked his apartment?"

"If by apartment you mean that shoebox on the next floor, then yes I have. He's not there."

"That _shoebox _is the home you gave him with the curse if I remember correctly," she pointed-out candidly. "And how do you know he's not there? He could just be in the shower or asleep or something."

"Well thank you for that insight, Sheriff Swan," Regina drawled, clearly unimpressed. "I used magic to let myself in and I can safely say that he's not there."

Emma rested her back against the sink and crossed an arm over her chest, her hand clasping her elbow. "You do realise that's breaking and entering, right? I can arrest you for that."

"I'd like to see you try," she challenged. "Now are you going to help locate Dr. Hopper or-"

The blonde sighed. "I'll be at his office in ten," she said, hanging up the phone.

She was sure that there was some reasonable explanation to Archie's apparent disappearance but if there was any truth to Regina's claims, Emma wouldn't be doing a good job as Sheriff or as a friend if she didn't follow it up.

But it was just so cold out.

And things had _finally _just started to settle down.

Emma huffed as she collected her coat and slinked her arms into the sleeves, praying that she had the patience to deal with the Evil Queen. Huh, that's something she never thought she'd ever hope for.

With her hand hovering over the door handle, she heard footsteps from behind her coming down the stairs and she turned to meet her mother's accusing eyes.

"Going somewhere?" Her voice was soft but displayed just a hint of that parental authoritative tone that Emma was so desperately trying to learn to use on Henry. It would seem that Mary Margaret had perfected it.

"Regina called. She said Archie's missing. I'm gonna go check it out."

She twisted around to open the door but her mother was quick to react, hopping down the last few steps and placing a hand on her shoulder. "Wait, he's missing? I'm going with you."

"What?"

Mary Margaret gathered her coat and hat and put them on as if against the clock. "Your father is out with Henry and I was hoping to spend some time with you today, so I'm coming with you. Besides, you might need back-up," she surmised with a small smile.

Emma's eyebrows shot up. "Back-up? What, against Regina? I think I can handle her." Mary Margaret fired a glance at her. Emma quickly continued, "It's just a routine check-up; I'll make a few inquiries, have a look around and see if I can figure out where Archie is. No big deal."

"Well, if it's no big deal then you won't mind if I tag along," she replied sharply as she opened the door and exited the apartment before Emma could summon a response.

The blonde shook her head at her mother's pro-active spirit. There was no point in arguing – she would win anyway. So, without complaint, she closed the door behind them.

"Just think of it as an adventure," Mary Margaret smiled.

"Yeah sure, whatever you say." Unfortunately, she couldn't suppress her smile either.

Maybe policing her with mom wouldn't be so bad.

* * *

Regina, in all her regal glory, was perched on the edge of the couch in Archie's office when Emma and Mary Margaret arrived. Of course the first thing she would think to do would be to make herself comfortable.

"Well it's about time you showed up Sheriff," she said, rising up to meet them. "Ah and I see you've brought your mother with you. Is that so she can hold your hand while you work?"

Emma narrowed her eyes briefly. "So why exactly are you here?"

Regina flicked her hair off her face and clucked her tongue. "I have a session with Dr. Hopper every day and we were scheduled to meet this afternoon. But when I arrived, he wasn't here and so I had a look around town and in his apartment only to find no trace of him. It's as though he's vanished into thin air."

"People don't just vanish into thin air," Emma remarked but then corrected herself, "Well, in Storybrooke I guess that's actually possible." Moving over to his desk, she rifled through his papers, trying to get a sense of the last thing he was reading. Nothing jumped out at her but she repeated the action over and over again as if somehow something would catch her eye.

"Wherever he is, he's without his jacket." That little tidbit was courtesy of Regina. At least she was observant.

"And he left in a hurry," Mary Margaret noted.

Emma put the papers back on the desk. "What makes you say that?"

She lifted up a lunchbox from the locker next to the window. "He didn't touch his lunch."

"That means nothing. He could be having it later."

"No, Dr. Hopper always takes a half-hour lunch at noon. We have our sessions at one."

The blonde sighed and took the box in her hands. "Are you sure he's not in Granny's? Or out for a walk?"

"Without his jacket?" her mother commented.

"Why would he go to Granny's when he already had lunch?" Her tone insinuated that Emma was an idiot. Sometimes she just wanted to punch her…

"Fine," she surrendered, "but where's Pongo? If he had been taken or whatever, the dog would still be here."

"Not unless they were trying to cover their tracks." Great, now her mom was a super sleuth. Just what her family needed – their own personal Sherlock Holmes. Did that make her Watson? Ugh, now her head hurt. Why couldn't Archie just walk through the door and proclaim himself alive and well? She didn't like to think that something bad had happened to him – Archie was a friend above all else – and the thought of something terrible befalling him created a knot in her stomach that only twisted with every passing moment.

They needed to find him.

"Okay so _maybe _something has happened, but I can't declare a missing person until twenty-four hours have passed. Until then we just keep an eye out for him."

"So your plan is to just…wait? There's been an abduction and you want to go and do whatever it is that you do? That sounds like a good plan Sheriff," the woman snarled sardonically. "I guess I'll just leave this little matter to you and the two idiots and hope that Dr. Hopper comes out of this ordeal alive." She started for the door.

"Why do you care so much Regina?"

Keeping her back to them, she spoke softly. "Because regardless of what you think of me Miss Swan, I do actually have a heart. I brought this town here and I ruled over it for twenty-eight years and I know all of its inhabitants. Dr. Hopper is one of only a few people who haven't treated me like the Evil Queen. And that is a luxury I would much rather keep." And with that she stalked out of the room, the sound of her heels clacking against the floor fading as she moved further away.

If there was one thing Emma admired about Regina, it was that she sure knew how to make an exit.

Mary Margaret shuffled beside the blonde and rubbed her hand lovingly along her arm. "We'll find him Emma. If there is one thing this family does, it's find the people that we care about. There's no one better for this job."

She sure hoped so.

* * *

With the help of David, Mary Margaret and Ruby, Emma searched all over Storybrooke for any sign of the doctor, but to no avail. An examination of his apartment for clues ended in more disappointment than enlightenment, a visit to Granny's for information proved useless as no one had seen or spoke to Archie since the previous day, and even Gepetto had nothing to tell them. It was looking like a hopeless case.

"I can't catch his scent," Ruby bemoaned, desperately sniffing his jacket. "Maybe he's underground."

"But we checked with the dwarves and they hadn't seen him," David answered, his hands placed firmly on his hips.

"He has to be in Storybrooke somewhere; he can't leave. We're just missing _something_." Hopeless situations seemed a common occurrence to Emma when she was younger; she always appeared to be fighting a losing battle or swimming against the tide, but giving-up was not in her vocabulary and she definitely wasn't ready to throw in the towel now. She was still the Sheriff – albeit to a land of Fairy Tale characters – and she was going to assert her authority and do everything she possibly could to find their friend.

She _was _Emma Swan after all. Finding people was what she did.

"Maybe we need to call it a night and start afresh in the morning?" Mary Margaret suggested.

It was getting pretty late. The moon hung ominously in the sky, casting a pale, ghostly shadow on the ground and the breeze was just cool enough to send a chill down the spine. Rain swept up the town, giving an extra bite to the menacing sky. Everything felt off balance, like there was a greater force at work, conspiring against them.

"No, wait," Emma instructed. "What about Gold? He can help us."

Ruby's eyes widened. "He can give us a potion like the one he gave you when you were trying to find Jefferson," she said to David.

The man smiled. "Right."

"You were trying to find Jefferson?" Mary Margaret questioned, tilting to her head to the side.

He nodded. "When you were both in the Enchanted Forest. I thought he could create a portal so I could get you home. Gold gave me a potion that led me to him."

"How?" Emma's natural scepticism liked to rear its head from time to time.

"I had to spill it over something that belonged to him. If we get the potion, we can sprinkle it over Archie's jacket and it should lead us to him."

"Then let's go!" Emma exclaimed, grabbing the opportunity with both hands.

Thumping the door to the shop, David called for the man. "Gold! Open up!"

After three more attempts, the door finally swung open revealing a tired-looking Rumpelstiltskin. "Oh, well if it isn't the new A-Team. What are you all doing here?"

"We need your help," Mary Margaret explained.

"Archie's missing and we need something to help us find him," Emma continued, trying to sound as friendly as possible. Though she knew it would be wasted on him.

Gold smirked. "And what exactly do you expect from me?"

Ruby spoke up. "A potion."

David, exuding his royal stature, moved in front of the group, his face mere inches from the other man. Emma couldn't help but be awed at her father. Every time he snapped into Prince mode, she felt herself utterly fascinated by the way he held himself. "Like the one you gave me. Back when I needed Jefferson's help."

"What makes you think I have something like that in my shop?"

"Because you like to keep things for a rainy day," her father emphasised.

With an impish chuckle, Gold raised a finger. "Wait here." He waded into his shop and returned a few moments later with a vile of navy liquid in his right hand. "Is this what you're looking for?" He dangled the vile in front of David's face like he was taunting a child with some candy.

"What's your price?" Emma demanded, fearing his request.

"Oh I don't know yet, Dearie. But let's just say that you'll owe me a favour. Do we have a deal?" His smile was too wide and Emma shuddered involuntarily.

The group exchanged glances with one another. "Deal," Emma stated.

"Here ya go!" Gold shoved the vile into David. "Now if you don't mind, it's getting late."

They backed away from his shop as he closed the door.

"Always a pleasure," Mary Margaret mumbled.

Ruby thrust Archie's jacket into the air, presenting it to the Prince. David uncorked the vile and with a deep breath and a glance at his family, he tossed the liquid all over the item of clothing, making sure to use all of it.

They waited.

Suddenly, the jacket glowed blue and escaped from Ruby's hands, flying wildly through the air, looping around in all directions. All of them chased after the cloth, following its tumultuous path. They ran for what felt like ages until the jacket plummeted onto the damp gravel in the middle of nowhere.

Gazing all around them, Emma stopped to catch her breath. She put her hands on her knees and inhaled deeply. "Well, where is he?" she quizzed in between breaths.

"I…I don't know," Ruby responded, sniffing the jacket again. "There's nothing around here."

"Maybe he's in the forest?" Mary Margaret offered.

"No the jacket should have led us right to him," David said angrily, squeezing his eyes shut and locking the bridge of his nose with his thumb and finger.

Emma yelled out for Archie and waited for an answer.

Nothing came.

All four of them called out at the top of their lungs, disturbing the wildlife.

Still nothing. Nothing but eerie silence.

"Now what?" Though she tried to fight it, Emma was getting tired.

"I think it's time we go home," her mother said quietly. "Try again in the morning."

"I'll keep his jacket and try to track him if I get a whiff of his scent." She had to admit, having a wolf as a friend was pretty handy in times of trouble.

"Thanks, Ruby."

Defeated and exhausted, the four of them ventured home, hoping that they'd have better luck in the morning but Emma couldn't help but wonder if they'd ever find out where he was. Gold's potion seemed a sure thing but now it looked as though nothing was a sure thing. The knot in her stomach twisted tighter.

Maybe tomorrow would be better.

It couldn't get any worse, right?

* * *

With Neal taking Henry out as a distraction for the day, Emma, Mary Margaret and David had their focus set on the search for Archie. They had rested well and decided on revisiting the area where the jacket had taken them the night before in the hopes of having the daylight on their side.

The drive was silent with each of them wrestling with their own thoughts. As they pulled up, Emma's phone buzzed and she eagerly answered it, thinking it news of Archie's whereabouts. Any news was good news, she told herself constantly.

"Hello?" she answered, breathless.

Mary Margaret and David listened intently to their daughter's side of the conversation, their eyes locking as they waited.

"Okay, we'll be right there." The blonde hung-up the phone.

"Emma, what is it?" her mother asked, worried.

Emma met her eyes in the rear-view mirror. "It's Ruby," she whispered. "She's missing."

**So now Ruby has joined the missing persons list! I hope to end each chapter in sort of a similar style – that is, of course, if people are interested in this idea! I'm really just experimenting to see how it goes! If you have any feedback or suggestions please do let me know! **

**What do you think happened to Archie? And Ruby? ;) **

**If you have time, please drop me a review and let me know what you thought! :)**


	2. Chapter 2

**Hello there! Hope you like what you read :)**

**Alas, I do not own OUAT.**

Mary Margaret's eyes were wide. Too wide. And sparking with unshed tears. "What do you mean Ruby's missing?" Her voice broke on the last word.

"That was Granny," Emma said, signalling to her phone, "She said Ruby didn't come home last night."

David twisted in his seat to face her. "But that's impossible. We walked her home."

"No, we didn't. We walked to the apartment and she went the rest of the way alone," the brunette interjected, panicked. "I knew we should brought her the whole way!"

"But it's not even a five minute walk?"

Emma looked back at her phone, scrutinizing the blank screen for answers. But she knew there'd be nothing there. "It doesn't matter. Whoever this person is they don't need much time to take action."

"Look we don't know if anything has happened to her yet, so let's not jump to conclusions." David: the voice of reason. "We'll go back to town and we'll follow procedure and take it from there." He faced the road once again and started the car, the engine roaring to life like an animal wakening from its slumber. The noise unnerved Emma.

"Okay one missing person is suspect enough but two? There has to be something going on here guys. I don't think we can just assume Ruby's acting out her rebellious teenage phase and staying out all night just for kicks."

The car took off down the road; chugging at first, it gained momentum as it picked up speed. "_Emma, _please," her father asserted, glancing over to his silent wife and taking her hand in his. The somewhat parental scold was not lost on Emma but instead of feeling small and embarrassed, she was fascinated by the unspoken communication between her parents. It was actually sort of beautiful – almost as if they were designed for one another.

Though she made no sound, Emma could tell that Mary Margaret was crying. She didn't need to be able to see her to know what was going on in her head. Ruby was her best friend and had been for years, and though they hadn't seen much of each other because of how crazy things were of late, they shared this unique bond that Emma could only describe as sisterly. They were family and they loved each other. Heck, she was pretty sure Ruby was even her godmother – yet no one had acknowledged that fact aloud.

But Ruby was a part of her family, too, and there was no way she was going to let her disappearance slip through the cracks. She and Archie were connected somehow – she just had to figure out how. And why. And then who was behind it.

One thing was for sure: she wasn't going to sit back and wait for the information to fall into her lap.

* * *

First stop: Granny's.

The morning glow of the rising sun had now dulled into a bleak blanket of grey cloud and Emma couldn't shake the feeling that it indicated a shift in their luck. And not in a good way.

Once they were all out of the car, Emma pulled her mother aside while David marched ahead into the diner.

"You okay?" she asked gently. The last thing she wanted was for her mother to be upset.

"I'm fine," the woman shrugged off.

"'Fine' doesn't really count, you know."

Mary Margaret narrowed her eyes. "People feel fine all the time."

"Yeah but they only say that when they're trying to hide how they're really feeling," she pointed out while keeping her voice as soft as possible. Well, for Emma, it still sounded pretty harsh but it was the thought that counted. Her mother sighed heavily. "Look, I know you're worried about Ruby. So am I. But we're going to find her. You have my word on that."

The brunette offered a small smile and clasped her hand around Emma's. "I know. I know we will." With a nod toward the diner, Mary Margaret led the blonde into the establishment, never letting go of her hand.

Seeing her mother so upset, so disconnected, served only to fuel Emma's desire to figure out what the hell was going on in Storybrooke and she made a silent vow to herself to do everything in her power to get to the bottom of it. After all, she was the Sheriff.

* * *

Granny's was abuzz with gossip. The usual dull chatter that occupied the booths was more of an electrical whirr of secrets and rumours companied with swift glances at the town's authority figures. Apparently news travelled fast in Storybrooke.

David was behind the counter intently discussing the details of Ruby's disappearance with her grandmother and over in the corner, Emma spied her son sharing what looked to be the ice cream sundae of death with the man who still made her want to punch something every time she thought about him. Sure she couldn't deny how much she liked seeing him spend time with Henry and watching them grow closer, but she was still angry at him and she wasn't sure when – or if – that would ever go away.

They looked as thick as thieves. How appropriate.

"Isn't it a bit early for ice cream?" she asked as she approached, kinking an eyebrow.

"Oh hey, Mom," the boy greeted, his mouth lathered in chocolate sauce. He didn't look one bit sheepish at being caught-out.

At least Neal did. He quickly reached across the table and yanked the dessert away from Henry, his brow furrowed. "It's mine," he said, shoving a spoonful into his mouth, "Henry was just having a bite. Sharing is caring, right?"

Emma narrowed her stare and smiled tightly.

"He can be very persuasive?" Neal scrunched his face. The kid laughed but at his father's not-so-subtle urging, he snatched at a napkin and cleaned up the evidence. "Personally I don't see the harm in it. Ice cream is a dairy product, you know, so it's practically good for him. Bone growth and all that."

"Nice try," the blonde smiled. She crossed her arms.

"Oh come on, Em. I remember a certain someone wishing she could have ice cream for breakfast all the time."

"_You _used to eat ice cream for breakfast?" Henry's eyes lit up at the prospect.

Great.

Emma sighed. "Once, that's all."

"It was more than once," Neal muttered under his breath but still loud enough that their kid could hear. Some things never change.

Henry glanced up at his mom and then back over to his dad. "So…are you guys ever going to tell me stories about when you were together?"

"No!" Emma and Neal exclaimed at the same time.

"Not right now, kid," Emma said, incredibly willing to move away from that particular subject for the time being. "I need to talk to Neal for a minute; why don't you go say hi to your grandparents?"

Henry shrugged and scooted out of the booth. Emma took his seat.

"I thought you guys were going to the park?" she asked.

"We are. I offered to bring him first thing but Henry wanted to go later because," he leaned in closer to her, "Grace will be there."

The blonde tilted her head to the side. "Grace? As in, Jefferson's daughter?"

"I think the kid has a crush on her," Neal suggested with a sly grin. "It's kinda cute actually."

"Oh I'm _so _not ready for him to be having crushes."

"Ah, I wouldn't worry too much about it. They're just kids." He took another bite of the sundae, his eyes never leaving her face. She hated when he did that; it was like he could read every thought she had ever had. "So I take it you didn't want to chat for no reason. What's up?"

Emma exhaled sharply. "Ruby's missing, too."

His tone was apologetic. "I heard. Gossip's like a contagious infection in this town. You got any leads?"

"I wish. I have no idea what's going on or where Archie and Ruby are and I can't shake the feeling that this is only the beginning."

"The beginning of what?"

She shook her head. "I don't know. Something bad."

"You'll figure it out, Em. You always do."

His sincerity took her off-guard and she dropped her eyes, self-conscious for the first time since they'd reunited.

"Either way, I need you to promise me that you won't let Henry out of your sight. Okay?"

"Do you mean like making sure to escort him to the bathroom-"

"Just promise me, Neal."

He raised his hands in surrender. "Okay, okay, I promise."

The relief rolled off her shoulders. "Thank you. I'll check in later."

"Looking forward to it," he winked with a chuckle.

* * *

David didn't get much out of Granny except that Ruby never came home the night before and hadn't answered her phone all night. Unfortunately that didn't give them much to go on.

With absolutely no indication of what may have happened, Mary Margaret, holding it together much better than earlier, suggested they retrace her steps from their apartment in the hope of finding _something _that would give them a lead – or at the very least, a direction to go.

They had just started when Emma's phone buzzed. She retrieved the device from her pocket, almost afraid to answer it in case of more bad news. She couldn't deal with any more right now.

She checked the name of the caller. Regina.

With a deep breath, she clicked 'answer'.

"It's nice to see your phone still works," Regina offered by way of greeting. Always such a pleasure to deal with.

"Excuse me?"

"From what I recall from our meeting yesterday you said you'd keep me informed about the investigation. Well, here we are a day later and I'm the one that has to make the call. Of course, I may overlook your slight in judgement if I found out your phone was broken but yet, it appears to be working accordingly."

Emma was so not in the mood for Regina's badgering. "What is it you want?"

"What I expected from you – an update on the case. Any ideas on Archie's whereabouts?"

The blonde sighed. "No, and Ruby's missing now as well. We think they're connected."

"Are you sure she didn't just take herself for a walk?" the woman sneered.

"Look, if you've only called to hurl insults and insinuations then you're holding up my time. I've got work to do, unless, you want to help in some way? You did say you cared about the people in this town…"

"That's not exactly what I meant, Sheriff. I've ruled over them; it is in my interest to find out what happened to them. I like to pride myself in knowing all about my people."

"We're not in the Enchanted Forest anymore Regina, and the last time I checked, you're no longer Mayor either. They are not your people."

Regina hesitated on the other end momentarily. "Have you spoken to Mr. Gold? He might have something that may help you locate them."

"Yeah, already did. He gave us some potion that David swore by but it only led us to some deserted road. Not really that helpful."

"Maybe it did work." The brunette's voice was distant almost, as if she was talking to herself.

"What do you mean?" David and Mary Margaret had gathered around the blonde now, eagerly listening to her.

"What I mean is that maybe the potion did work – but only to a certain extent. Perhaps something was hindering it from working further."

"Like what? Some magical force field?"

"Perhaps."

It made sense, in a way. The jacket went in all kinds of directions before just dying out in the middle of nowhere. There could have been a different reason for that. "So you're saying that we should be looking for someone…magical?"

"No, not exactly. Just someone who has access to magic."

"Which just so happens to be everyone in town," Emma scoffed. "Magic is not exactly hard to come by here."

"Well I'm sorry I couldn't be of any more help to you, Sheriff." She sounded annoyed but Emma didn't care. "But I will do some digging of my own and see what I can uncover."

Emma swallowed. "Thanks, Regina." For some reason, she hated saying those words.

They may not have been any closer to figuring out where Ruby and Archie were but with Regina helping, they may just have the upper hand. And that was enough for Emma right now.

* * *

The rest of the day went by with little or no progress in the case and Emma was becoming more frustrated as the day rolled on. She just wanted one little thing, one little lead that she could follow and occupy her time with. But nothing came.

Waiting for Henry to be dropped off by Neal, her mother made her a hot chocolate and she soothed her chagrin with the smooth liquid, letting it coat her insides.

Just as she was finishing the drink, Henry burst through the front door, his bangs matted to his forehead.

"Henry? What is it?" Emma rushed over to him, bending down to his level.

Neal came bounding behind him with a distraught Grace in tow.

"What's going on?" she fired at them.

Grace sniffed and wiped the tears off her face. "It's my Papa."

_Don't say it_, Emma prayed to herself.

"He's gone."

**Dun, dun, dun! Poor Jefferson! Hope you enjoyed what you read! Any thoughts or feedback would be greatly appreciated :) **


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